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Woodchip bioreactors are viable low-cost nitrate (NO₃⁻) removal applications for treating agricultural and aquaculture discharges. The active microbial biofilms growing on woodchips are conducting nitrogen (N) removal, reducing NO₃⁻ while oxidizing the carbon (C) from woodchips. However, bioreactor age, and changes in the operating conditions or in the microbial community might affect the NO₃⁻ removal as well as potentially promote nitrous oxide (N₂O) production through either incomplete denitrification or dissimilatory NO₃⁻ reduction to ammonium (DNRA). Here, we combined stable isotope approach, amplicon sequencing, and captured metagenomics for studying the potential NO₃⁻ removal rates, and the abundance and community composition of microbes involved in N transformation processes in the three different full-scale woodchip bioreactors treating recirculating aquaculture system (RAS …